A just food system transformation is imperative to meet this century’s goals of environmental sustainability, economic fairness, and equitable social well-being. While considerations of justice are beginning to inform food system transformation debates, there remains a lack of conceptual and practical integration of these two historically separate disciplinary perspectives. This perspective therefore proposes the just transformation matrix (JUSTRA), which integrates justice and transformation concerns using an interrogative approach. Interrogatives probe the historical, present, and future intersections of justice with specific food system elements. If used conscientiously, the JUSTRA can assist a wide spectrum of food system actors in strategizing, implementing, and monitoring just food system transformations. It can also help stakeholders to more thoughtfully engage with power imbalances both among users and in the food system more broadly—if used “in bona fides.” Thus, while further testing is necessary to fully realize the potential of the JUSTRA, the matrix can become a powerful tool in multi-stakeholder dialogues to navigate unpredictable, diverse, and power-laden complexities of just food system transformations.